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Attenuation

Repository source: Attenuation

Description

This MRI image illustrates attenuation that can occur due to sensor position. The artifact is removed by dividing by the attenuation profile determined manually. This histograms shows how the artifact hides information in the form of scalar value clusters.

Info

See this figure in Chapter 10 the VTK Textbook.

Other languages

See (Python), (PythonicAPI)

Question

If you have a question about this example, please use the VTK Discourse Forum

Code

Attenuation.cxx

#include <vtkImageActor.h>
#include <vtkImageCast.h>
#include <vtkImageGaussianSmooth.h>
#include <vtkImageMapper3D.h>
#include <vtkImageMathematics.h>
#include <vtkImageProperty.h>
#include <vtkImageReader2.h>
#include <vtkImageReader2Factory.h>
#include <vtkImageShiftScale.h>
#include <vtkInteractorStyleImage.h>
#include <vtkNamedColors.h>
#include <vtkNew.h>
#include <vtkRenderWindow.h>
#include <vtkRenderWindowInteractor.h>
#include <vtkRenderer.h>
#include <vtkSampleFunction.h>
#include <vtkSphere.h>

int main(int argc, char* argv[])
{

  // Verify input arguments.
  if (argc != 2)
  {
    std::cout << "Usage: " << argv[0]
              << " Filename e.g. AttenuationArtifact.pgm" << std::endl;
    return EXIT_FAILURE;
  }

  // Read the image
  vtkNew<vtkImageReader2Factory> readerFactory;
  vtkSmartPointer<vtkImageReader2> reader;
  reader.TakeReference(readerFactory->CreateImageReader2(argv[1]));
  reader->SetFileName(argv[1]);

  vtkNew<vtkImageCast> cast;
  cast->SetInputConnection(reader->GetOutputPort());
  cast->SetOutputScalarTypeToDouble();

  // Get rid of discrete scalars.
  vtkNew<vtkImageGaussianSmooth> smooth;
  smooth->SetInputConnection(cast->GetOutputPort());
  smooth->SetStandardDeviations(0.8, 0.8, 0);

  vtkNew<vtkSphere> m1;
  m1->SetCenter(310, 130, 0);
  m1->SetRadius(0);

  vtkNew<vtkSampleFunction> m2;
  m2->SetImplicitFunction(m1);
  m2->SetModelBounds(0, 264, 0, 264, 0, 1);
  m2->SetSampleDimensions(264, 264, 1);

  vtkNew<vtkImageShiftScale> m3;
  m3->SetInputConnection(m2->GetOutputPort());
  m3->SetScale(0.000095);

  vtkNew<vtkImageMathematics> div;
  div->SetInputConnection(0, smooth->GetOutputPort());
  div->SetInputConnection(1, m3->GetOutputPort());
  div->SetOperationToMultiply();

  // Create actors.
  vtkNew<vtkNamedColors> colors;

  double colorWindow = 256.0;
  double colorLevel = 127.5;
  vtkNew<vtkImageActor> originalActor;
  originalActor->GetMapper()->SetInputConnection(cast->GetOutputPort());
  originalActor->GetProperty()->SetColorWindow(colorWindow);
  originalActor->GetProperty()->SetColorLevel(colorLevel);

  vtkNew<vtkImageActor> filteredActor;
  filteredActor->GetMapper()->SetInputConnection(div->GetOutputPort());

  // Define viewport ranges.
  // (xmin, ymin, xmax, ymax)
  double originalViewport[4] = {0.0, 0.0, 0.5, 1.0};
  double filteredViewport[4] = {0.5, 0.0, 1.0, 1.0};

  // Setup renderers.
  vtkNew<vtkRenderer> originalRenderer;
  originalRenderer->SetViewport(originalViewport);
  originalRenderer->AddActor(originalActor);
  originalRenderer->ResetCamera();
  originalRenderer->SetBackground(colors->GetColor3d("SlateGray").GetData());

  vtkNew<vtkRenderer> filteredRenderer;
  filteredRenderer->SetViewport(filteredViewport);
  filteredRenderer->AddActor(filteredActor);
  filteredRenderer->ResetCamera();
  filteredRenderer->SetBackground(
      colors->GetColor3d("LightSlateGray").GetData());

  vtkNew<vtkRenderWindow> renderWindow;
  renderWindow->SetSize(600, 300);
  renderWindow->AddRenderer(originalRenderer);
  renderWindow->AddRenderer(filteredRenderer);
  renderWindow->SetWindowName("Attenuation");

  vtkNew<vtkRenderWindowInteractor> renderWindowInteractor;
  vtkNew<vtkInteractorStyleImage> style;

  renderWindowInteractor->SetInteractorStyle(style);

  renderWindowInteractor->SetRenderWindow(renderWindow);
  renderWindow->Render();
  renderWindowInteractor->Initialize();

  renderWindowInteractor->Start();

  return EXIT_SUCCESS;
}

CMakeLists.txt

cmake_minimum_required(VERSION 3.12 FATAL_ERROR)

project(Attenuation)

find_package(VTK COMPONENTS 
  CommonColor
  CommonCore
  CommonDataModel
  IOImage
  ImagingCore
  ImagingGeneral
  ImagingHybrid
  ImagingMath
  InteractionStyle
  RenderingContextOpenGL2
  RenderingCore
  RenderingFreeType
  RenderingGL2PSOpenGL2
  RenderingOpenGL2
)

if (NOT VTK_FOUND)
  message(FATAL_ERROR "Attenuation: Unable to find the VTK build folder.")
endif()

# Prevent a "command line is too long" failure in Windows.
set(CMAKE_NINJA_FORCE_RESPONSE_FILE "ON" CACHE BOOL "Force Ninja to use response files.")
add_executable(Attenuation MACOSX_BUNDLE Attenuation.cxx )
  target_link_libraries(Attenuation PRIVATE ${VTK_LIBRARIES}
)
# vtk_module_autoinit is needed
vtk_module_autoinit(
  TARGETS Attenuation
  MODULES ${VTK_LIBRARIES}
)

Download and Build Attenuation

Click here to download Attenuation and its CMakeLists.txt file. Once the tarball Attenuation.tar has been downloaded and extracted,

cd Attenuation/build

If VTK is installed:

cmake ..

If VTK is not installed but compiled on your system, you will need to specify the path to your VTK build:

cmake -DVTK_DIR:PATH=/home/me/vtk_build ..

Build the project:

make

and run it:

./Attenuation

WINDOWS USERS

Be sure to add the VTK bin directory to your path. This will resolve the VTK dll's at run time.